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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgtttcctctatacacactttgtgtgatcaaatgttacatttttctgattttggttaactctttttttttttggattctgaattcttcatagctt...

Basic information

species Arabidopsis thaliana
transcript AT2G39390.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39390.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G43770.1 (Glycine max), 5'ss of exon 2
AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgta-tgtgtttcctctatacacactttgtgtgatcaaatgttacatttttctgattttggttaactctttttttttttggattctgaattcttcatagctt
| |||||||| | |  |||| |||||||  | ||||| ||||||||  | |||||||| ||||||||||| || ||||| ||||| ||||||||||||||||| |    ||  ||||   |  | | || |       | ||     |||  | |||  ||| |   | | || ||||| | | |||  | | ||      
AGGCTGATCTGTTGAATCAGCTGAAGGACCTCAAGGCCGAGCTTGCCTTGCTTCGTGTTGCTAAGGTCACCGGCGGTGCACCTAACAAGCTCTCTAAGATgtaataatcttaatctaataattcctcgtttc------tcttttgcctttgaggtttgtgttta---tgtgttattttgaaat-tgaggtttgcag-----

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G38480.1 (Glycine max), 5'ss of exon 2
AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgtttcctctatacacactttgtgtgatcaaatgttacatttttctgattttggttaactctttttttttttggattctgaattcttcatagctt
| ||||||||   |  |||  |||||||  | ||||| ||||||||  | |||||||| ||||||||||| || ||||| ||||| ||||| || ||||||||      |  |||| | | | |||   |  |      |   |  | | || | ||  |||  | ||||    || || ||   |              
AGGCTGATCTGCTGAATCAACTGAAGGACCTGAAGGCGGAGCTTGCCTTGCTTCGTGTTGCTAAGGTCACCGGTGGTGCCCCTAACAAGCTTTCCAAGATgtaataacctaatctaaataaatttttgtttgttttgcctatgaggtgtttg-tgttaattacttattttgaaattggggtttgcag-------------

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv06s0004g04020.t01 (Vitis vinifera), 5'ss of exon 3
AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgtttcctctatacacactttgtgtgatcaaatgttacatttttctgatt-ttggttaactctttttttttttggattctgaattcttcatagctt
| || ||||| | ||  || ||||||||  | || |||||||| ||||| || || ||||| ||||||||||| |||||||| || ||||| |||||||||||  |  || |||| |      | | | |       | | | |||      | | || | |  ||       | |    |     |    ||  ||  | 
AGGCCGATCTGTTGGCCCAATTGAAGGAGCTGAAAGCAGAGCTCGCTCTTCTCCGAGTCGCCAAGGTCACTGGTGGTGCTCCCAACAAGCTTTCTAAGATgtac-tactttctctctgttttatatttatatgtgtttatcaaattgactaaactgtttggttgctgagagaatctggaaaggaaaagaaattggtaagtg

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv00s0317g00130.t01 (Vitis vinifera), 5'ss of exon 2
AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgtttcctctatacacactttgtgtgatcaa--atgttacatttttctgattttggttaactctttttttttttggattctgaattcttcatagctt
| || ||  | | ||  ||||||||||| || ||||| || |||||||| || || || || |||||||| || ||||| || || |||||||| ||||||||     ||   || | |    | ||| |    |    ||||| || | | |  ||   |||   |     ||| || |  ||        ||  |||   
AGGCGGACTTGTTGGTGCAGTTGAAGGAGTTGAAGGCCGAACTTGCTCTTCTCCGAGTTGCCAAGGTCACCGGTGGTGCACCAAACAAGCTCTCCAAGATgtactctcttttcctcttccatttatgtatatatatctgtgttatatgtgtatttttcaagttttgttaagatttattggtgtttatgcggtttgttagg--

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S6_426V6.1 (Physcomitrella patens), 5'ss of exon 3
AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgtttcctctatacacactttgtgtgatcaaatgttacatttttctgattttggttaactctttttttttttggattctgaattcttcatagctt-------
                     | |||||  | || || |||||||||   ||  | ||||| |||||||||||||| |||||||| ||||| ||||||||||| |   |||     | | | ||| ||    |  | || |      |  |  |  |||     | | ||   ||  |       ||||||    ||| |       
--------------------CTCAAGGAGCTAAAAGCTGAGCTTGCTGCTCTGAGAGTCGCAAAGGTCACTGGAGGCGCTCCTAACAAGCTGTCTAAGATgtacgc--ttctctcgtcctcccttggttgattgtattgctgtgaaatattcttcatggccggttgtgttaactt--gagcgtctaattctc---agcctgaaaaat

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125027239|gb|EL099508.1|EL099508
EST:     CTCCTAATAAGCTCTCTAAGAT                         CAAGGTGGTGAGGAAGTCGATTGCTCAGGTGTTGACAGTGATCTCACAGAA
genomic: CTCCTAATAAGCTCTCTAAGATgtatgtgttt ... ttgatttcagCAAGGTGGTGAGGAAGTCGATTGCTCAGGTGTTGACAGTGATCTCACAGAA
EST: gi|86076065|gb|DR371822.1|DR371822
EST:     CTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGAT                         CAAGGTGGTGAGGAAGTCGATTGCTCAGGTGTTGACAGTGATCTCACAGAA
genomic: CTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgttt ... ttgatttcagCAAGGTGGTGAGGAAGTCGATTGCTCAGGTGTTGACAGTGATCTCACAGAA
EST: gi|164138312|gb|ES133447.1|ES133447
EST:     GTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGAT                         CAAGGTGGTGAGGAAGTCGATTGC
genomic: GTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgttt ... ttgatttcagCAAGGTGGTGAGGAAGTCGATTGC
EST: gi|164004075|gb|ES216042.1|ES216042
EST:     GTCGCTAAGGTCACTGGAGGTGCTACCTAATAAGCTCTCTAAGAT                         CAAGGTGGTGAGGAAGTCGATTGC
genomic: GTCGCTAAGGTCACTGGAGGTGCT-CCTAATAAGCTCTCTAAGATgtatgtgttt ... ttgatttcagCAAGGTGGTGAGGAAGTCGATTGC
EST: gi|152038390|gb|AV821605.2|AV821605
EST:     CTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGAT                         CAAGGTGGTGAGGAAGTCGATTGCTCAGGTGTTGACAGTGATCTCACAGAA
genomic: CTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgttt ... ttgatttcagCAAGGTGGTGAGGAAGTCGATTGCTCAGGTGTTGACAGTGATCTCACAGAA
EST: gi|125228882|gb|EL242967.1|EL242967
EST:     CTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGAT                         CAAGGTGGTGAGGAAGTCGATTGCTCAGGTGT
genomic: CTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgttt ... ttgatttcagCAAGGTGGTGAGGAAGTCGATTGCTCAGGTGT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTGATCTTTCGGGTCAGTTGAAGGAATTTAAGGCAGAGCTTGCTCTCCTTCGTGTCGCTAAGGTCACTGGAGGTGCTCCTAATAAGCTCTCTAAGATgtatgtgtttcctctatacacactttgtgtgatcaaatgttacatttttctgattttggttaactctttttttttttggattctgaattcttcatagctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttttt